PaperclipOrg
Claude Agent Skill · by Mims Harvard

Tooluniverse Sequence Retrieval

Install Tooluniverse Sequence Retrieval skill for Claude Code from mims-harvard/tooluniverse.

Install
Terminal · npx
$npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-sequence-retrieval
Works with Paperclip

How Tooluniverse Sequence Retrieval fits into a Paperclip company.

Tooluniverse Sequence Retrieval drops into any Paperclip agent that handles this kind of work. Assign it to a specialist inside a pre-configured PaperclipOrg company and the skill becomes available on every heartbeat — no prompt engineering, no tool wiring.

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Source file
SKILL.md148 lines
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---name: tooluniverse-sequence-retrievaldescription: Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles. Creates detailed reports with sequence metadata, cross-database references, and download options. Use when users need nucleotide sequences, protein sequences, genome data, or mention GenBank, RefSeq, EMBL accessions.--- # Biological Sequence Retrieval Retrieve DNA, RNA, and protein sequences with proper disambiguation and cross-database handling. **IMPORTANT**: Always use English terms in tool calls. Only try original-language terms as fallback. Respond in the user's language. **LOOK UP DON'T GUESS**: Never assume accession numbers or sequence versions. Always retrieve and verify from NCBI or ENA. ## Domain Reasoning Sequence quality hierarchy: RefSeq (NM_/NP_ = curated) > RefSeq predicted (XM_/XP_) > GenBank (submitted). Prefer the MANE Select transcript for human canonical isoforms. Check version numbers -- annotations improve across versions. ## Workflow ```Phase 0: Clarify (if needed) → Phase 1: Disambiguate Gene/Organism → Phase 2: Search & Retrieve → Phase 3: Report``` --- ## Phase 0: Clarification (When Needed) Ask ONLY if: gene exists in multiple organisms, sequence type unclear, or strain matters.Skip for: specific accessions, clear organism+gene combos, complete genome requests with organism. --- ## Phase 1: Gene/Organism Disambiguation ### Accession Type Decision Tree | Prefix | Type | Use With ||--------|------|----------|| NC_/NM_/NR_/NP_/XM_ | RefSeq | NCBI only || U*/M*/K*/X*/CP*/NZ_ | GenBank | NCBI or ENA || EMBL format | EMBL | ENA preferred | **CRITICAL**: Never try ENA tools with RefSeq accessions -- they return 404. ### Identity Checklist- Organism confirmed (scientific name)- Gene symbol/name identified- Sequence type determined (genomic/mRNA/protein)- Accession prefix identified for tool selection --- ## Phase 2: Data Retrieval (Internal) Retrieve silently. Do NOT narrate the search process. ```python# Search NCBI Nucleotideresult = tu.tools.NCBI_search_nucleotide(    operation="search", organism=organism, gene=gene,    strain=strain, keywords=keywords, seq_type=seq_type, limit=10) # Get accessions from UIDsaccessions = tu.tools.NCBI_fetch_accessions(operation="fetch_accession", uids=result["data"]["uids"]) # Retrieve sequence (FASTA or GenBank format)sequence = tu.tools.NCBI_get_sequence(operation="fetch_sequence", accession=accession, format="fasta") # ENA alternative (non-RefSeq accessions only)entry = tu.tools.ena_get_entry(accession=accession)fasta = tu.tools.ena_get_sequence_fasta(accession=accession)``` ### Fallback Chains | Primary | Fallback | Notes ||---------|----------|-------|| NCBI_get_sequence | ENA (if GenBank format) | NCBI unavailable || ENA_get_entry | NCBI_get_sequence | ENA doesn't have RefSeq || NCBI_search_nucleotide | Try broader keywords | No results | --- ## Phase 3: Report Sequence Profile Present as a **Sequence Profile Report**. Hide search process. Include: 1. **Search Summary**: query, database, result count2. **Primary Sequence**: accession, type (RefSeq/GenBank), organism, strain, length, molecule, topology, curation level3. **Sequence Preview**: first lines of FASTA (truncated)4. **Annotations Summary**: CDS/tRNA/rRNA/regulatory feature counts (from GenBank format)5. **Alternative Sequences**: ranked by relevance and curation, with ENA compatibility6. **Cross-Database References**: RefSeq, GenBank, ENA/EMBL, BioProject, BioSample7. **Download Options**: FASTA (for BLAST/alignment), GenBank (for annotation) ### Curation Level Tiers | Tier | Prefix | Description ||------|--------|-------------|| RefSeq Reference (best) | NC_, NM_, NP_ | NCBI-curated, gold standard || RefSeq Predicted | XM_, XP_, XR_ | Computationally predicted || GenBank Validated | Various | Submitted, some curation || GenBank Direct | Various | Direct submission || Third Party | TPA_ | Third-party annotation | --- ## Reasoning Framework **Sequence quality**: Prefer RefSeq over GenBank. Check version numbers. Sequences with "PREDICTED" in definition are not experimentally validated. **Accession guidance**: RefSeq = NCBI-only. GenBank = mirrored in ENA/EMBL. Default to RefSeq mRNA (NM_) for human/model organisms; most complete genome assembly for microbial queries. **Cross-database reconciliation**: Same sequence may have different accessions (e.g., GenBank U00096 = RefSeq NC_000913 for E. coli K-12). Always report both when available. Discrepancies between GenBank/RefSeq typically indicate RefSeq curation corrected submission errors. ### Synthesis Questions1. What is the highest-quality accession available?2. Are there alternative accessions in other databases?3. What is the annotation completeness?4. Is the sequence from the expected organism/strain?5. What download format suits the user's downstream analysis? --- ## Error Handling | Error | Response ||-------|----------|| "No search criteria provided" | Add organism, gene, or keywords || "ENA 404 error" | Likely RefSeq -- use NCBI only || "No results found" | Broaden search, check spelling, try synonyms || "Sequence too large" | Note size, provide download link instead | --- ## Tool Reference **NCBI Tools**: `NCBI_search_nucleotide` (search), `NCBI_fetch_accessions` (UID→accession), `NCBI_get_sequence` (retrieve)**ENA Tools (GenBank/EMBL only)**: `ena_get_entry` (metadata), `ena_get_sequence_fasta` (FASTA), `ena_get_entry_summary` (summary) --- ## Search Parameters Reference **NCBI_search_nucleotide**: `operation`="search", `organism` (scientific name), `gene` (symbol), `strain`, `keywords`, `seq_type` (complete_genome/mrna/refseq), `limit` **NCBI_get_sequence**: `operation`="fetch_sequence", `accession`, `format` (fasta/genbank)